Method of combing an elongated molecule

ABSTRACT

Elongated molecules are stretched across a substrate by controlled fluid flow.

CROSS-REFERENCE TO RELATED APPLICATIONS

The present application is related to and claims the benefit of theearliest available effective filing date(s) from the following listedapplication(s) (the “Related Applications”) (e.g., claims earliestavailable priority dates for other than provisional patent applicationsor claims benefits under 35 USC §119(e) for provisional patentapplications, for any and all parent, grandparent, great-grandparent,etc. applications of the Related Application(s)).

Related Applications:

-   -   For purposes of the USPTO extra-statutory requirements, the        present application constitutes a continuation-in-part of U.S.        patent application Ser. No. 11/480,763, entitled METHOD OF        COMBING AN ELONGATED MOLECULE, naming Roderick A. Hyde and        Lowell L. Wood, Jr.; as inventors, filed Jun. 30, 2006 now U.S.        Pat. No. 7,312,029, which is currently, or is an application of        which a currently application is entitled to the benefit of the        filing date.    -   For purposes of the USPTO extra-statutory requirements, the        present application constitutes a continuation-in-part of U.S.        patent application Ser. No. 11/480,779, entitled METHOD OF        APPLYING AN ELONGATED MOLECULE TO A SURFACE, naming Roderick A.        Hyde and Lowell L. Wood, Jr.; as inventors, filed Jun. 30, 2006        now U.S. Pat. No. 7,595,150, which is currently, or is an        application of which a currently application is entitled to the        benefit of the filing date.    -   For purposes of the USPTO extra-statutory requirements, the        present application constitutes a continuation-in-part of U.S.        patent application Ser. No. 11/480,820, entitled METHOD OF        COMBING A NUCLEIC ACID, naming Roderick A. Hyde and Lowell L.        Wood, Jr.; as inventors, filed Jun. 30, 2006, which is currently        co-pending, or is an application of which a currently co-pending        application is entitled to the benefit of the filing date.    -   For purposes of the USPTO extra-statutory requirements, the        present application constitutes a continuation-in-part of U.S.        patent application Ser. No. 11/502,584 entitled METHOD OF        COMBING A NUCLEIC ACID, naming Roderick A. Hyde and Lowell L.        Wood, Jr.; as inventors, filed Aug. 9, 2006 now U.S. Pat. No.        7,618,771, which is currently, or is an application of which a        currently application is entitled to the benefit of the filing        date.

The United States Patent Office (USPTO) has published a notice to theeffect that the USPTO's computer programs require that patent applicantsreference both a serial number and indicate whether an application is acontinuation or continuation-in-part. Stephen G. Kunin, Benefit ofPrior-Filed Application, USPTO Official Gazette Mar. 18, 2003, availableat http://www.uspto.gov/web/offices/com/sol/og/2003/week11/patbene.htm.The present applicant entity has provided above a specific reference tothe application(s)from which priority is being claimed as recited bystatute. Applicant entity understands that the statute is unambiguous inits specific reference language and does not require either a serialnumber or any characterization, such as “continuation” or“continuation-in-part,” for claiming priority to U.S. patentapplications. Notwithstanding the foregoing, applicant entityunderstands that the USPTO's computer programs have certain data entryrequirements, and hence applicant entity is designating the presentapplication as a continuation-in-part of its parent applications as setforth above, but expressly points out that such designations are not tobe construed in any way as any type of commentary and/or admission as towhether or not the present application contains any new matter inaddition to the matter of its parent application(s). All subject matterof the Related Applications and of any and all parent, grandparent,great-grandparent, etc. applications of the Related Applications isincorporated herein by reference to the extent such subject matter isnot inconsistent herewith.

SUMMARY

In one aspect, a method of forming a nanowire includes applying anucleic acid-containing solution to a first substrate that has a definedphysical feature thereon, controllably flowing the nucleicacid-containing solution over the first substrate in a manner thatpromotes stretching of a nucleic acid molecule from the defined physicalfeature along the substrate, and applying a conductive material to thestretched nucleic acid molecule to form a nanowire. The nucleic acid maybe DNA (e.g., mtDNA or cDNA), RNA (e.g., mRNA, tRNA, miRNA, or rRNA), ora synthetic nucleic acid (e.g., PNA, LNA, GNA, or TNA), may includechromosomes, viruses, plasmids, oligonucleotides, double-strandednucleic acids, or single-stranded nucleic acids, and/or may be bound toa nanotube. The defined physical feature may be, for example, adepression or a protrusion. The substrate may include a plurality ofdefined physical features (e.g., in a repeating array), and nucleic acidmolecules may extend from at least a subset of the plurality along thesubstrate. The method may further include transferring the stretchednucleic acid molecule to a second substrate, before or after applyingthe conductive material. Transferring may include bringing the first andsecond substrates into proximity or into contact, and may includecontrolling a surface charge of either or both substrates, where thesurface charge may be attractive or repulsive, and may be spatiallyand/or temporally patterned. Alternatively or in addition, transferringmay include controlling surface energy, temperature, and/orhydrophilicity of one or both of the substrates. The conductive materialmay be, for example, a metal, a semiconductor, a compound, or a polymer,and it may be substantially contiguous. The method may include applyinga cover surface to the nucleic acid-containing solution, in which casecontrollably flowing may include moving the cover surface relative tothe first substrate, for example by peeling or sliding the coversurface. The first substrate and/or the cover surface (if present) mayinclude surface features that spatially direct the fluid flow, such asmicro-orifices or switchable channels. The fluid that flows through themicro-orifices or switchable channels may be a liquid (such as thenucleic acid-containing solution) or a gas. Controllably flowing mayinclude inducing surface charges (e.g., static, dynamic, and/orspatially patterned charges) on the first substrate and/or the coversurface (if present), for example by photoinducing surface charges.Alternatively or in addition, controllably flowing may include applyinga varying surface tension (which may be temporally or spatially varied),applying an electromagnetic field (e.g., a pure electric field, a puremagnetic field, a plasmon, a static field, a dynamic field, and/or aspatially patterned field), controlling hydrophilicity (e.g., by varyinghydrophilicity spatially and/or temporally), or varying temperature, andmay include inducing vorticity into the nucleic acid-containing solution(which may promote deposition of a nucleic acid molecule in a curvealong the first substrate). The nucleic acid-containing solution mayinclude a mechanical anchor having a nucleic acid molecule anchoredthereto, where the defined physical feature acts to spatially fix themechanical anchor. The defined physical feature may include an anchorednucleic acid strand which hybridizes to a nucleic acid molecule in thenucleic acid-containing solution, in which case the method may furtherinclude dehybridizing the anchored strand and the hybridized nucleicacid.

In another aspect, a method of applying a nucleic acid to a surfaceincludes applying a nucleic acid-containing solution to a firstsubstrate having a defined physical feature including a nucleic acidanchor, and controllably flowing a deposition fluid (e.g., the nucleicacid-containing solution) over the first substrate in a manner thatpromotes stretching of a nucleic acid molecule from the defined physicalfeature along the first substrate. The nucleic acid may be DNA (e.g.,mtDNA or cDNA), RNA (e.g., mRNA, tRNA, miRNA, or rRNA), or a syntheticnucleic acid (e.g., PNA, LNA, GNA, or TNA), may include chromosomes,viruses, plasmids, oligonucleotides, double-stranded nucleic acids, orsingle-stranded nucleic acids, and/or may be bound to a nanotube. Thenucleic acid anchor may include an anchor strand of nucleic acidattached to the first substrate, which may hybridize with a nucleic acidmolecule from the nucleic acid-containing solution. The nucleicacid-containing solution and/or the deposition solution may include anucleic acid molecule bound to a mechanical anchor (e.g., a bead), andthe nucleic acid anchor may include a trap (e.g., a depression or aprotrusion) for the mechanical anchor. The trap may physically,electrically, and/or magnetically trap the mechanical anchor, and/or mayadhere to it. The defined physical feature may be, for example, adepression or a protrusion. The substrate may include a plurality ofdefined physical features (e.g., in a repeating array), and nucleic acidmolecules may extend from at least a subset of the plurality along thesubstrate. The method may further include transferring the stretchednucleic acid molecule to a second substrate, and may include applying aconductive material to the stretched nucleic acid molecule to form ananowire, either before or after transferring the stretched nucleic acidmolecule. Transferring may include bringing the first and secondsubstrates into proximity or into contact, and may include controlling asurface charge of either or both substrates, where the surface chargemay be attractive or repulsive, and may be spatially and/or temporallypatterned. The second substrate may include an electronic device inelectrical communication with the transferred nucleic acid molecule. Themethod may further include attaching an electronic device to thetransferred nucleic acid molecule. The method may further includecontrolling a surface charge of the first substrate, where thecontrolled surface charge acts to attract and/or to repel the nucleicacid molecule from the first substrate. Controllably flowing may includeapplying a cover surface to the deposition fluid, and may furtherinclude moving the cover surface relative to the first substrate, forexample by peeling or sliding the cover surface. The first substrateand/or the cover surface (if present) may include surface features thatspatially direct the fluid flow, such as micro-orifices or switchablechannels. The fluid that flows through the micro-orifices or switchablechannels may be a liquid (such as the nucleic acid-containing solutionand/or the deposition solution) or a gas. Controllably flowing mayinclude inducing surface charges (e.g., static, dynamic, and/orspatially patterned charges) on the first substrate and/or the coversurface (if present), for example by photoinducing surface charges.Alternatively or in addition, controllably flowing may include applyinga varying surface tension (which may be temporally or spatially varied),applying an electromagnetic field (e.g., a pure electric field, a puremagnetic field, a plasmon, a static field, a dynamic field, and/or aspatially patterned field), controlling hydrophilicity (e.g., by varyinghydrophilicity spatially and/or temporally), or varying temperature, andmay include inducing vorticity into the deposition fluid (which maypromote deposition of a nucleic acid molecule in a curve along thesubstrate).

In a further aspect, a method of applying an elongated molecule to asurface includes controllably flowing a solution containing an elongatedmolecule over a first substrate in a manner that promotes stretching theelongated molecule from a defined physical feature along the firstsubstrate. The elongated molecule is selected from the group consistingof polymers (e.g., isotactic polymers, atactic polymers, stereotacticpolymers, thermoplastics, thermosets, elastomers, copolymers, blockcopolymers, organic polymers, inorganic polymers, polyamides,polyesters, polycarbonates, polyethers, polyimides, polyimines,formaldehydes, polysulfones, polyurethanes, polyvinyls, polyolefins,and/or polyalkynes), nanotubes, proteins (e.g., antibodies, enzymes,hormones, structural proteins, regulatory proteins, filamentousproteins, soluble proteins, motor proteins, denatured proteins, and/orpolypeptides), carbohydrates (e.g., monosaccharides, disaccharides,oligosaccharides, polysaccharides, starches, glycogens, cellulose,amylose, and/or chitin), lipids (e.g. fatty acids, glycerides,phosphoglycerides, sphingolipids, steroids, waxes, lipoproteins, and/orglycolipids), and functionalized forms of any of the above. The definedphysical feature may be, for example, a depression or a protrusion. Thefirst substrate may include a plurality of defined physical features(e.g., in a repeating array), and elongated molecules may extend from atleast a subset of the plurality along the substrate. The method mayfurther include applying a conductive material (e.g., a metal, asemiconductor, a compound, and/or a polymer) to the stretched elongatedmolecule. The conductive material may be substantially contiguous. Themethod may further include transferring the stretched elongated moleculeto a second substrate. A conductive material (e.g., a metal, asemiconductor, a compound, and/or a polymer) may be applied to thestretched elongated molecule before or after transfer, and theconductive material may be substantially contiguous. Transferring mayinclude bringing the first and second substrates into proximity or intocontact, and may include controlling a surface charge of either or bothsubstrates, where the surface charge may be attractive or repulsive, andmay be spatially and/or temporally patterned. Alternatively or inaddition, transferring may include controlling surface energy,temperature, and/or hydrophilicity of one or both of the substrates. Thesecond substrate may include an electronic device in electroniccommunication with the transferred elongated molecule. The method mayfurther include attaching an electronic device to the transferredelongated molecule. The method may include applying a cover surface tothe solution, in which case controllably flowing may include moving thecover surface relative to the first substrate, for example by peeling orsliding the cover surface. The first substrate and/or the cover surface(if present) may include surface features that spatially direct thefluid flow, such as micro-orifices or switchable channels. The fluidthat flows through the micro-orifices or switchable channels may be aliquid (such as the solution containing the elongated molecule) or agas. Controllably flowing may include inducing surface charges (e.g.,static, dynamic, and/or spatially patterned charges) on the firstsubstrate and/or the cover surface (if present), for example byphotoinducing surface charges. Alternatively or in addition,controllably flowing may include applying a varying surface tension(which may be temporally or spatially varied), applying anelectromagnetic field (e.g., a pure electric field, a pure magneticfield, a plasmon, a static field, a dynamic field, and/or a spatiallypatterned field), controlling hydrophilicity (e.g., by varyinghydrophilicity spatially and/or temporally), or varying temperature, andmay include inducing vorticity into the solution (which may promotedeposition of an elongated molecule in a curve along the firstsubstrate). The solution may include a mechanical anchor (e.g., a bead)having the elongated molecule anchored thereto, and the defined physicalfeature may act to spatially fix the mechanical anchor (e.g., byphysically trapping, electrically trapping, magnetically trapping,and/or adhering to the mechanical anchor).

In yet another aspect, a method of applying an elongated molecule to asurface includes applying a solution containing the elongated moleculeto a first substrate, and controllably flowing a deposition fluid overthe first substrate in a manner that promotes stretching of theelongated molecule along the first substrate. Controllably flowing thedeposition fluid includes flowing the deposition fluid in aconfiguration in which a surface of the deposition fluid isunconstrained. The elongated molecule may be a polymer (e.g., isotacticpolymers, atactic polymers, stereotactic polymers, thermoplastics,thermosets, elastomers, copolymers, block copolymers, organic polymers,inorganic polymers, polyamides, polyesters, polycarbonates, polyethers,polyimides, polyimines, formaldehydes, polysulfones, polyurethanes,polyvinyls, polyolefins, and/or polyalkynes), a nanotube, a protein(e.g., antibodies, enzymes, hormones, structural proteins, regulatoryproteins, filamentous proteins, soluble proteins, motor proteins,denatured proteins, and/or polypeptides), a carbohydrate (e.g.,monosaccharides, disaccharides, oligosaccharides, polysaccharides,starches, glycogens, cellulose, amylose, and/or chitin), a lipid (e.g.,fatty acids, glycerides, phosphoglycerides, sphingolipids, steroids,waxes, lipoproteins, and/or glycolipids), a nucleic acid (e.g.,chromosomes, viruses, plasmids, oligonucleotides, naturally-occurringnucleic acids, synthetic nucleic acids, double-stranded nucleic acids,single-stranded nucleic acids, DNA, RNA, PNA, LNA, GNA, TNA, and/ornucleic acids bound to nanotubes), or a functionalized form of any ofthe above. The first substrate may include at least one defined physicalfeature, and controllably flowing may promote stretching of theelongated molecule from the defined physical feature along the firstsubstrate. The first substrate may include a plurality of definedphysical features (e.g., in a repeating array), where a plurality ofelongated molecules may extend from at least a subset of the pluralityof defined physical features along the first substrate. The method mayfurther include transferring the stretched elongated molecule to asecond substrate. A conductive material (e.g., a metal, a semiconductor,a compound, and/or a polymer) may be applied to the stretched elongatedmolecule before or after transfer, and the conductive material may besubstantially contiguous. Transferring may include bringing the firstand second substrates into proximity or into contact, and may includecontrolling a surface charge of either or both substrates, where thesurface charge may be attractive or repulsive, and may be spatiallyand/or temporally patterned. The second substrate may include anelectronic device in electronic communication with the transferredelongated molecule. The method may further include attaching anelectronic device to the transferred elongated molecule. The depositionfluid may be the solution containing the elongated molecule. The firstsubstrate may include surface features that spatially direct the fluidflow, such as micro-orifices or switchable channels. The fluid thatflows through the micro-orifices or switchable channels may be a liquid(such as the solution containing the elongated molecule and/or thedeposition fluid) or a gas. Controllably flowing may include inducingsurface charges (e.g., static, dynamic, and/or spatially patternedcharges) on the first substrate, for example by photoinducing surfacecharges. Alternatively or in addition, controllably flowing may includeapplying a varying surface tension (which may be temporally or spatiallyvaried), applying an electromagnetic field (e.g. a pure electric field,a pure magnetic field, a plasmon, a static field, a dynamic field,and/or a spatially patterned field), controlling hydrophilicity (e.g.,by varying hydrophilicity spatially and/or temporally), or varyingtemperature, and may include inducing vorticity into the solution (whichmay promote deposition of an elongated molecule in a curve along thefirst substrate).

In still another aspect, a method of applying an elongated molecule to asurface includes applying a solution containing the elongated moleculeto a first substrate, and controllably flowing a deposition fluid overthe first substrate in a manner that promotes stretching of theelongated molecule along the first substrate. Controllably flowing thedeposition fluid includes flowing the deposition fluid in aconfiguration in which a surface of the deposition fluid maintains asubstantially fixed distance from the first substrate. The elongatedmolecule may be a polymer (e.g., isotactic polymers, atactic polymers,stereotactic polymers, thermoplastics, thermosets, elastomers,copolymers, block copolymers, organic polymers, inorganic polymers,polyamides, polyesters, polycarbonates, polyethers, polyimides,polyimines, formaldehydes, polysulfones, polyurethanes, polyvinyls,polyolefins, and/or polyalkynes), a nanotube, a protein (e.g.,antibodies, enzymes, hormones, structural proteins, regulatory proteins,filamentous proteins, soluble proteins, motor proteins, denaturedproteins, and/or polypeptides), a carbohydrate (e.g., monosaccharides,disaccharides, oligosaccharides, polysaccharides, starches, glycogens,cellulose, amylose, and/or chitin), a lipid (e.g., fatty acids,glycerides, phosphoglycerides, sphingolipids, steroids, waxes,lipoproteins, and/or glycolipids), a nucleic acid (e.g., chromosomes,viruses, plasmids, oligonucleotides, naturally-occurring nucleic acids,synthetic nucleic acids, double-stranded nucleic acids, single-strandednucleic acids, DNA, RNA, PNA, LNA, GNA, TNA, and/or nucleic acids boundto nanotubes), or a functionalized form of any of the above. The firstsubstrate may include at least one defined physical feature, andcontrollably flowing may promote stretching of the elongated moleculefrom the defined physical feature along the first substrate. The firstsubstrate may include at least one defined physical feature, andcontrollably flowing may promote stretching of the elongated moleculefrom the defined physical feature along the first substrate. The firstsubstrate may include a plurality of defined physical features (e.g., ina repeating array), where a plurality of elongated molecules may extendfrom at least a subset of the plurality of defined physical featuresalong the first substrate. The method may further include transferringthe stretched elongated molecule to a second substrate. A conductivematerial (e.g., a metal, a semiconductor, a compound, and/or a polymer)may be applied to the stretched elongated molecule before or aftertransfer, and the conductive material may be substantially contiguous.Transferring may include bringing the first and second substrates intoproximity or into contact, and may include controlling a surface chargeof either or both substrates, where the surface charge may be attractiveor repulsive, and may be spatially and/or temporally patterned. Thesecond substrate may include an electronic device in electroniccommunication with the transferred elongated molecule. The method mayfurther include attaching an electronic device to the transferredelongated molecule. The deposition fluid may be the solution containingthe elongated molecule. The method may include applying a cover surfaceto the solution, in which case controllably flowing may include movingthe cover surface relative to the first substrate, for example bysliding the cover surface. The first substrate and/or the cover surface(if present) may include surface features that spatially direct thefluid flow, such as micro-orifices or switchable channels. The fluidthat flows through the micro-orifices or switchable channels may be aliquid (such as the solution containing the elongated molecule and/orthe deposition fluid) or a gas. Controllably flowing may includeinducing surface charges (e.g. static, dynamic, and/or spatiallypatterned charges) on the first substrate and/or the cover surface (ifpresent), for example by photoinducing surface charges. Alternatively orin addition, controllably flowing may include applying a varying surfacetension (which may be temporally or spatially varied), applying anelectromagnetic field (e.g., a pure electric field, a pure magneticfield, a plasmon, a static field, a dynamic field, and/or a spatiallypatterned field), controlling hydrophilicity (e.g., by varyinghydrophilicity spatially and/or temporally), or varying temperature, andmay include inducing vorticity into the solution (which may promotedeposition of an elongated molecule in a curve along the firstsubstrate).

The foregoing summary is illustrative only and is not intended to be inany way limiting. In addition to the illustrative aspects, embodiments,and features described above, further aspects, embodiments, and featureswill become apparent by reference to the drawings and the followingdetailed description.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 is a flowchart illustrating methods of placing elongatedmolecules on a substrate.

FIG. 2 shows a solution of elongated molecules applied to a substrate.

FIG. 3 shows a cover surface applied to the solution of FIG. 2.

FIG. 4 shows stretching of the elongated molecules along the substrate.

FIG. 5 shows an irregular arrangement of stretched elongated molecules.

FIG. 6 shows a regular arrangement of stretched elongated molecules.

FIG. 7 shows stretched elongated molecules on a first substrate beingtransferred to a second substrate.

FIG. 8 shows a cover surface including a plurality of micro-orifices.

FIG. 9 shows a cover surface including a plurality of switchablechannels.

FIG. 10 shows a switchable channel layout.

FIG. 11 shows a plurality of stretched elongated molecules bound to aplurality of mechanical anchors.

FIG. 12 shows a single-stranded nucleic acid used as an anchor.

FIG. 13 shows a bead bound to a single-stranded nucleic acid used as ananchor.

FIG. 14 shows a solution of free elongated molecules applied to asubstrate.

FIG. 15 shows a deposition fluid containing a plurality of mechanicalanchors applied to the solution of FIG. 14.

FIG. 16 shows the mechanical anchors of FIG. 15 bound to the elongatedmolecules and trapped at the substrate.

DETAILED DESCRIPTION

In the following detailed description, reference is made to theaccompanying drawings, which form a part hereof. In the drawings,similar symbols typically identify similar components, unless contextdictates otherwise. The illustrative embodiments described in thedetailed description, drawings, and claims are not meant to be limiting.Other embodiments may be utilized, and other changes may be made,without departing from the spirit or scope of the subject matterpresented here.

FIG. 1 illustrates several embodiments of methods of placingnanometer-scale arrangements of elongated molecules on a substrate.Broadly, the methods include applying a solution of elongated moleculesto a first substrate (block 100), and controllably flowing a depositionfluid (which may be the solution of elongated molecules) over the firstsubstrate to stretch the elongated molecules (block 120). In someembodiments, the elongated molecules may be metallized or otherwiserendered conductive by application of a conductive material (block 160).In these or other embodiments, the elongated molecules may betransferred to a second substrate (block 140), for example using softlithography techniques (see, e.g., Rogers, et al., “Recent progress insoft lithography,” Mat. Today, 8(2):50-56 (February 2005), which isincorporated herein by reference). When the elongated molecules aremetallized or otherwise coated with a conductive composition, thiscoating may occur before or after the transfer to the second substrate.In some embodiments, the elongated molecules may be attached to anelectronic device (block 170).

One method for producing nanometer-scale arrays of DNA molecules ispresented in Guan, et al., “Generating highly ordered DNA nanostrandarrays,” Proc. Nat'l Acad. Sci., 102(51):18321-18325 (December 2005),which is incorporated herein by reference. As shown therein, aDNA-containing solution is deposited on a glass slide, and a flexiblepoly(dimethyl siloxane) (PDMS) stamp is applied to the solution. Whenthe flexible stamp is peeled away from the substrate, the DNA in thesolution elongates along and adheres to the stamp, creating anarrangement of parallel strands. (This process is referred to as“combing” the DNA.) The stamp is patterned with an array of depressions,so that the DNA extends along the stamp from one depression to the next.The stamp is then applied to another surface, transferring the DNAthereto. The transferred DNA may be arranged in a regular array of fixedlength strands corresponding to the spacing of the depressions on thestamp.

While the method presented in Guan focuses on application of DNAnanostrands to a substrate, for example for large-scale and highlyautomated analysis, the combed DNA strands may also be metallized (orcoated with a nonmetallic conductor) to produce a regular array ofnanoscale conductive segments. (In other embodiments, elongatedmolecules other than nucleic acids may be used, which may beintrinsically conductive.) This array may be used as a sort of“nanoscale breadboard” for construction of nanoscale circuits. In someembodiments, the regular array may mimic traditional breadboard layouts,while in others it may differ, for example to facilitate uniquerequirements of nanoscale circuits. The ability to position nucleic acidstrands of known sequence, as further discussed below, may facilitateself-assembly of complex circuits by allowing circuit elements to bebound to known locations on a substrate.

In particular, in some embodiments, the arrangements of elongatedmolecules may be connected to the nanotube-based transistors and othercircuit elements described in copending and commonly owned U.S. patentapplication Ser. No. 11/314,738, filed Dec. 20, 2005 and entitled“Deletable Nanotube Circuit,” Ser No. 11/314,718, filed Dec. 20, 2005and entitled “Connectible Nanotube Circuit,” and Ser No. 11/314,751,filed Dec. 20, 2005 and entitled “Nanotube Circuit Analysis System andMethod,” all of which are incorporated herein by reference. In someembodiments, nanotube-based circuit elements may be “wrapped” withhelical nucleic acids, as described in Heller, et al., “OpticalDetection of DNA Conformational Polymorphism on Single-Walled CarbonNanotubes,” Science 311:508-511, January 2006, which is incorporatedherein by reference. These elements may then be selectively placed atdesired locations on a “breadboard” substrate as described above, byhybridization with nucleic acids fixed at selected locations on thesurface to self-assemble a circuit. Rothemund, “Folding DNA to createnanoscale shapes and patterns,” Nature 440:297-302, March 2006,incorporated herein by reference, describes another self-assemblytechnique in which structures are created having localized nucleic acidsequences. These structures may be used as nucleic acid anchors (furtherdiscussed below) for placement of nucleic acid molecules to be “combed,”or as guides for placement of nanotube-based circuit elements.

A variety of elongated molecules may be applied to substrates asdiscussed below, such as nucleic acid molecules, including withoutlimitation DNA such as mtDNA or cDNA, RNA such as mRNA, tRNA, miRNA, orrRNA, synthetic nucleic acids such as PNA, LNA, GNA, or TNA,chromosomes, viruses, plasmids, and oligonucleotides, any of which maybe in single-stranded or double-stranded form, and any of which may bebound to other structures such as nanotubes (for example, a DNA-wrappednanotube is described in Heller, supra), may be applied to substrates asdiscussed below. Other elongated molecules that may be applied to asubstrate in the same manner include polymers (e.g., isotactic polymers,atactic polymers, stereotactic polymers, thermoplastics, thermosets,elastomers, copolymers, block copolymers, organic polymers, inorganicpolymers, polyamides, polyesters, polycarbonates, polyethers,polyimides, polyimines, formaldehydes, polysulfones, polyurethanes,polyvinyls, polyolefins, and/or polyalkynes), nanotubes, proteins (e.g.,antibodies, enzymes, hormones, structural proteins, regulatory proteins,filamentous proteins, soluble proteins, motor proteins, denaturedproteins, and/or polypeptides), carbohydrates (e.g., monosaccharides,disaccharides, oligosaccharides, polysaccharides, starches, glycogens,cellulose, amylose, and/or chitin), lipids (e.g., fatty acids,glycerides, phosphoglycerides, sphingolipids, steroids, waxes,lipoproteins, and/or glycolipids), or modified or functionalized formsof any of these.

Application of the solution of elongated molecules to the firstsubstrate may include anchoring the elongated molecules to the substrate(block 102), for example by anchoring them to defined physical featuresof the substrate. In some embodiments, the elongated molecules mayadhere directly to the substrate (block 104). In other embodiments, theelongated molecules may adhere to anchors which are affixed to thesubstrate (block 106). In still other embodiments, the elongatedmolecules may be attached (block 108) to mechanical anchors (e.g.,beads) in the solution (or in a separate deposition fluid), and thoseanchors may be trapped at the substrate (block 110) by a variety ofmeans (e.g., physically, chemically, electrically, and/or magnetically).

Controlled flow over the first substrate stretches the elongatedmolecules along the substrate (block 120), usually but not necessarilyalong the path of controlled flow over the substrate. A variety ofmethods are contemplated for controlling flow. In some embodiments, acover surface is applied to the solution containing the elongatedmolecules (block 122). This surface may then be moved (block 124) tocontrollably flow the solution (e.g., by peeling it away from thesubstrate or sliding it along the substrate). Alternatively or inaddition, the cover surface may comprise channels or micro-orifices, anda deposition fluid (which may be the solution of elongated molecules)may be flowed through the channels or orifices (block 126). In otherembodiments, a deposition fluid may flow across the substrate (block128). Flow (in the solution or in another deposition fluid) may also becontrolled by inducing patterns in surface charge, surface tension,hydrophilicity, applied electromagnetic field, and/or temperature.

Optionally, the stretched elongated molecules may be transferred to asecond substrate (block 140). In some embodiments, this transfer may befacilitated or controlled by application of surface charges to the firstand/or the second substrate (block 142). Conductive material may beapplied to the elongated molecules either before or after transfer(block 160), and an electronic device (e.g., a transistor such as acarbon nanotube transistor) may be attached to the stretched elongatedmolecule (block 170) before or after any transfer and before or afterany application of conductive material.

FIGS. 2-16 illustrate several exemplary embodiments of theabove-described methods. These examples should be consideredillustrative only, as many other configurations of the described methodswill be apparent to those skilled in the art.

As shown in FIG. 2, a solution 10 containing elongated molecules 16 isapplied to a first substrate 12 having defined physical features 14. Thesolution is controllably flowed over the first substrate in a mannerthat promotes stretching of an elongated molecule 16 from the definedphysical feature along the first substrate. In the embodiment shown inFIG. 3 and FIG. 4, this flow is accomplished by applying cover slip 18to the solution 10 and sliding it along the first substrate 12 whilemaintaining a constant distance between the cover slip and thesubstrate, inducing flow parallel to the substrate 12. (Equivalently,the substrate may be moved while the cover surface is held still;“moving the cover surface relative to the substrate” is considered toinclude all configurations in which cover surface and/or substrate aremoved relative to one another.) In other embodiments, this flow may beinduced or controlled by other methods, and may involve a separatedeposition fluid as discussed below. A conductive material (e.g., ametal, a semiconductor, a polymer, or a compound) may then be applied tothe stretched elongated molecule 16 to form a nanowire. (The stretchedmolecules 16 may be transferred to a second substrate, as discussedbelow in connection with FIG. 7, either before or after the applicationof conductive material.) In some embodiments, the conductive coating mayform a contiguous coating around the elongated molecule, while in otherembodiments, the coating may be partial.

Defined physical features 14 may be distributed randomly on the firstsubstrate 12 as shown in FIG. 5, in an ordered array as shown in FIG. 6,or in any other suitable arrangement for a particular embodiment. In theordered array shown in FIG. 6, the defined features 14 are anarrangement of depressions. Elongated molecules 16 extend from eachdepression to an adjacent one. As discussed in Guan et al. (supra), ifnucleic acid molecules are transferred to another substrate (e.g. bysoft lithography), portions extending from one depression to the nextmay be selectively transferred to produce a regular array of nucleicacid molecules having a substantially uniform length. Other types ofmolecules may be similarly transferred, and other defined physicalfeatures such as protrusions and chemical or mechanical anchors may alsobe used.

FIG. 7 illustrates the process of transferring elongated molecules 16from the first substrate 12 to a second substrate 20, by placing thesubstrates in proximity to one another. (In Guan et al. (supra), thePDMS stamp was allowed to dry, and then was placed in contact with aflat surface for one minute.) In some embodiments, transfer from thefirst substrate 12 to the second substrate 20 may be enhanced bymanipulating properties of either or both substrates such as the surfaceenergy, the surface charge, the temperature, and/or the hydrophilicityof the substrates, or by the application of an electromagnetic field(e.g., a pure electric field, a pure magnetic field, a static field, adynamic field, a spatially patterned field, and/or a plasmon). Forexample, a photoinduced surface charge may be used to repel theelongated molecules 16 from the first substrate 12, and/or to attractthe elongated molecules to the second substrate 20, to enhance transfer.These surface charges may be uniform across the substrate(s), or theymay be spatially patterned to enhance or inhibit transfer in localizedareas. Depending on the properties of the substrates, transfer may occureven without direct contact between the first and second substrates.

FIG. 8 illustrates an alternate embodiment for controllably flowing thesolution over the first substrate. As shown, a cover surface 22including a plurality of micro-orifices 24 is applied to the solution onthe first substrate. A deposition fluid flowing through themicro-orifices 24 controls the flow of the solution. The depositionfluid may be the solution containing the elongated molecules, or it maybe a separate fluid (which may be a liquid or a gas). In someembodiments, flow in the micro-orifices may be controlled bymanipulating their surface charge, surface energy, temperature, and/orhydrophilicity, or by application of electromagnetic fields (e.g., apure electric field, a pure magnetic field, a static field, a dynamicfield, a spatially patterned field, and/or a plasmon).

FIG. 9 and FIG. 10 illustrate an additional embodiment for controllablyflowing the solution over the first substrate. As shown in FIG. 9, acover surface 26 including a plurality of channels 28 is applied to thesolution on the first substrate. A detail of a channel 28 layout isshown in FIG. 10; however, many layouts are possible depending on thedesired final arrangement of elongated molecules. A deposition fluidflowing through the channels controls the flow of the solution. Thedeposition fluid may be the solution containing the elongated molecules,or it may be a separate fluid (which may be a liquid or a gas). In someembodiments, flow in the channels may be controlled by manipulatingtheir surface charge, surface energy, temperature, and/orhydrophilicity, or by application of electromagnetic fields (e.g., apure electric field, a pure magnetic field, a static field, a dynamicfield, a spatially patterned field, and/or a plasmon).

In some embodiments, flow along the first substrate may be controlled bymanipulating the surface charge, surface energy, temperature, and/orhydrophilicity of the first substrate, even if the solution has a freesurface, for example by photoinducing surface charges. Alternatively orin addition, flow may be controlled by similarly manipulating theproperties of a cover slip such as that shown in FIG. 3 and FIG. 4.Electromagnetic fields (e.g., a pure electric field, a pure magneticfield, a static field, a dynamic field, a spatially patterned field,and/or a plasmon) may also be used to control flow, with or without acover slip.

In some embodiments, controlling flow includes maintaining a laminarflow, while in other embodiments, controlling flow includes inducingvorticity into the solution. In either of these embodiments, elongatedmolecules may be deposited in a curve along the substrate. In someembodiments, the deposition fluid that is controllably flowed across thesubstrate may be the solution containing the elongated molecules, whilein others, a separate deposition fluid may be used to “comb” themolecules after the solution has been placed on the substrate.

In another embodiment, illustrated in FIG. 11, elongated molecules 16 insolution may be bound to physical anchors 30 (such as beads). Thesebeads may be trapped by the defined physical features 14 on the firstsubstrate, shown in FIG. 11 as depressions that mechanically trap thebeads. In other embodiments, the defined physical features mayelectrically or magnetically trap the physical anchors, or may adhere tothe physical anchors (e.g., by hydrogen bonds, polar bonds, ionic bonds,dipole attraction, and/or covalent bonds). In some embodiments, thisconfiguration may provide nucleic acid molecules or proteins having aknown sequence at the surface of the substrate (since the molecules maybe anchored to the bead at a known point in their sequence).

As shown in FIG. 12, the defined physical features 14 at the surface ofthe first substrate may be single stranded nucleic acids bound to thefirst substrate 12. In another embodiment, shown in FIG. 13, singlestranded nucleic acids may be bound to physical anchors such as beads30, which are trapped by the defined physical features 14 of the firstsubstrate as described in connection with FIG. 11. In either of theseembodiments, when a nucleic acid-containing solution is controllablyflowed across the first substrate, the localized strands (bound to thesubstrate or to the physical anchor) may then hybridize withcomplementary nucleic acids in the solution, anchoring the nucleic acidsin place at one end (from which they may extend across the firstsubstrate in the direction of the flow of the solution). Thisconfiguration may also provide nucleic acid molecules having a knownsequence on the surface of the substrate, since the localized strandsmay have known sequences which will bind to specific sequences withinthe nucleic acid-containing solution. In some embodiments, thehybridized stretched nucleic acid molecule may then be dehybridized. Forexample, the hybridized stretched nucleic acid molecule may bedehybridized when a second substrate is brought into contact with (orinto the vicinity of) the first substrate to facilitate transfer to thesecond substrate. In some such embodiments, the first substrate and itslocalized single strand anchors may be reusable.

In another embodiment, shown in FIG. 14, a solution 10 containingelongated molecules 16 is applied to a first substrate 12 having definedphysical features 14. A deposition fluid 32 containing mechanicalanchors 34 is controllably flowed over the first substrate, as shown inFIG. 15 and FIG. 16. As the deposition fluid is flowed across thesubstrate, the mechanical anchors 34 bind to the elongated molecules 16and are trapped by the defined physical features 14, which thus act asnucleic acid anchors. The elongated molecules extend from the trappedmechanical anchors 34 along the substrate as the deposition fluid flows.

While various aspects and embodiments have been disclosed herein, otheraspects and embodiments will be apparent to those skilled in the art.The various aspects and embodiments disclosed herein are for purposes ofillustration and are not intended to be limiting, with the true scopeand spirit being indicated by the following claims.

1. A method of applying an elongated molecule to a surface, comprising:applying a solution containing the elongated molecule to a firstsubstrate; controllably flowing a deposition fluid over the firstsubstrate in a manner that promotes stretching of the elongated moleculealong the first substrate; and applying a conductive material to thestretched elongated molecule to form a nanowire, wherein controllablyflowing the deposition fluid comprises flowing the deposition fluid in aconfiguration in which a surface of the deposition fluid isunconstrained.
 2. The method of claim 1, wherein the elongated moleculeis selected from the group consisting of polymers, nanotubes, proteins,carbohydrates, lipids, nucleic acids, and functionalized forms of any ofthe above.
 3. The method of claim 2, wherein the elongated molecule is apolymer selected from the group consisting of isotactic polymers,atactic polymers, stereotactic polymers, thermoplastics, thermosets,elastomers, copolymers, block copolymers, organic polymers, inorganicpolymers, polyamides, polyesters, polycarbonates, polyethers,polyimides, polyimines, formaldehydes, polysulfones, polyurethanes,polyvinyls, polyolefins, and polyalkynes.
 4. The method of claim 2,wherein the elongated molecule is a protein selected from the groupconsisting of antibodies, enzymes, hormones, structural proteins,regulatory proteins, filamentous proteins, soluble proteins, motorproteins, denatured proteins, and polypeptides.
 5. The method of claim2, wherein the elongated molecule is a carbohydrate selected from thegroup consisting of monosaccharides, disaccharides, oligosaccharides,polysaccharides, starches, glycogens, cellulose, amylose, and chitin. 6.The method of claim 2, wherein the elongated molecule is a lipidselected from the group consisting of fatty acids, glycerides,phosphoglycerides, sphingolipids, steroids, waxes, lipoproteins, andglycolipids.
 7. The method of claim 2, wherein the elongated molecule isa nucleic acid selected from the group consisting of chromosomes,viruses, plasmids, oligonucleotides, naturally-occurring nucleic acids,synthetic nucleic acids, double-stranded nucleic acids, andsingle-stranded nucleic acids.
 8. The method of claim 2, wherein theelongated molecule is a nucleic acid selected from the group consistingof DNA, RNA, PNA, LNA, GNA, and TNA.
 9. The method of claim 2, whereinthe elongated molecule is a nucleic acid bound to a nanotube.
 10. Themethod of claim 1, wherein the first substrate has at least one definedphysical feature, and wherein controllably flowing promotes stretchingof the elongated molecule from the defined physical feature along thefirst substrate.
 11. The method of claim 1, further comprisingtransferring the stretched elongated molecule to a second substrate. 12.The method of claim 11, wherein transferring the stretched elongatedmolecule to the second substrate comprises bringing the first substratein proximity to the second substrate.
 13. The method of claim 12,wherein bringing the first substrate in proximity to the secondsubstrate comprising bringing the first substrate into contact with thesecond substrate.
 14. The method of claim 11, further comprisingcontrolling a surface charge of the second substrate, wherein thesurface charge acts to attract the elongated molecule to the secondsubstrate.
 15. The method of claim 14, further comprising controlling asurface charge of the first substrate, wherein the surface charge actsto attract the elongated molecule to the first substrate.
 16. The methodof claim 14, wherein controlling a surface charge of the secondsubstrate includes inducing a spatiotemporally patterned charge on thesecond substrate.
 17. The method of claim 11, further comprisingcontrolling a surface charge of the first substrate, wherein the surfacecharge acts to repel the elongated molecule from the first substrate.18. The method of claim 17, further comprising controlling a surfacecharge of the second substrate, wherein the surface charge acts toattract the elongated molecule to the second substrate.
 19. The methodof claim 17, further comprising controlling a surface charge of thesecond substrate, wherein the surface charge acts to repel the elongatedmolecule from the second substrate.
 20. The method of claim 17, whereincontrolling a surface charge of the first substrate includes creating aspatially patterned surface charge on the first substrate.
 21. Themethod of claim 11, further comprising controlling a surface charge ofthe second substrate, wherein the surface charge is spatially patterned.22. The method of claim 11, further comprising controlling a surfacecharge of the second substrate, wherein the surface charge is dynamic.23. The method of claim 11, further comprising controlling a surfacecharge of the second substrate, wherein the surface charge is static.24. The method of claim 11, wherein the second substrate comprises anelectronic device, and wherein the transferred elongated molecule is inelectrical communication with the electronic device.
 25. The method ofclaim 11, further comprising attaching an electronic device to thetransferred elongated molecule.
 26. The method of claim 1, wherein thedeposition fluid is the solution containing the elongated molecule. 27.The method of claim 1, wherein the first substrate comprises surfacefeatures that spatially direct fluid flow.
 28. The method of claim 1,wherein the first substrate comprises a plurality of micro-orifices, andwherein controllably flowing comprises flowing a fluid through at leasta subset of the micro-orifices.
 29. The method of claim 28, wherein thefluid that flows through the at least a subset of the micro-orifices isthe solution containing the elongated molecule.
 30. The method of claim28, wherein the fluid that flows through the at least a subset of themicro-orifices is the deposition fluid.
 31. The method of claim 28,wherein the fluid that flows through the at least a subset of themicro-orifices is a gas.
 32. The method of claim 1, wherein the firstsubstrate comprises a plurality of switchable channels, and whereincontrollably flowing comprises switching at least a subset of theswitchable channels.
 33. The method of claim 1, wherein controllablyflowing comprises inducing vorticity in the deposition fluid.
 34. Themethod of claim 33, wherein the fluid flow promotes deposition of theelongated molecule in a curve along the first substrate.
 35. The methodof claim 1, wherein controllably flowing comprises directing fluid flowby applying a varying surface tension along the first substrate.
 36. Themethod of claim 35, wherein the surface tension is temporally varied.37. The method of claim 35, wherein the surface tension is spatiallyvaried.
 38. The method of claim 1, wherein controllably flowingcomprises directing fluid flow by applying an electromagnetic field tothe deposition fluid.
 39. The method of claim 38, wherein theelectromagnetic field is a pure electric field.
 40. The method of claim38, wherein the electromagnetic field is a pure magnetic field.
 41. Themethod of claim 38, wherein the electromagnetic field is a static field.42. The method of claim 38, wherein the electromagnetic field is adynamic field.
 43. The method of claim 38, wherein the electromagneticfield is spatially patterned.
 44. The method of claim 1, whereincontrollably flowing comprises directing fluid flow by controllinghydrophilicity of the first substrate.
 45. The method of claim 44,wherein controlling hydrophilicity of the first substrate comprisesdynamically changing the hydrophilicity of the first substrate.
 46. Themethod of claim 1, wherein controllably flowing comprises controllingthe temperature of the deposition fluid.